Multi-Omics Analysis Reveals the Gut-Mediated Mechanism Underlying the Seasonal Non-Laying Phenotype in Zhedong White Geese (Anser cygnoides domesticus)

As a precious indigenous goose resource in China, the Zhedong white goose occupies an essential position in the domestic goose industry. However, this breed spontaneously enters a prolonged non-laying period of over two months per year, which greatly limits egg production capacity and restricts the economic development of the goose industry. Herein, this study systematically compared serum physiological indices and serum and fecal metabolome, as well as fecal microbial communities, between laying and non-laying Zhedong white geese, aiming to reveal the key regulatory mechanisms underlying reproductive stage transition. Physiological analyses indicated that non-laying geese had higher serum levels of GnRH, PRL, APOA, and T-AOC, whereas the concentrations of LH, E2, TNF-α, IL-1, and calcium were significantly reduced; FSH, PROG, and BA levels showed no significant differences between the two groups. Metabolomic analysis identified 277 upregulated and 403 downregulated DAMs in feces, and 386 DAMs in serum. The shared enriched pathways across serum and fecal samples encompassed arginine biosynthesis, histidine metabolism, and pantothenate and CoA biosynthesis, as well as steroid hormone biosynthesis. A total of 120 DAMs overlapped in two specimens, and the non-laying geese presented pronounced depletion of tryptophan-derived metabolites and steroid hormone-related metabolites. Metagenomic results showed no significant difference in gut microbial alpha diversity between groups, while their microbial community structures were clearly differentiated. A total of 774 upregulated and 854 downregulated microbial species were screened in non-laying geese, and these differential microbes were primarily enriched in pathways associated with reproductive hormone signaling, steroid biosynthesis and energy metabolism. Multi-omics correlation analysis verified close associations between differential microbes and reproductive-related metabolites. Certain probiotic strains, including Pediococcus pentosaceus and Lactococcus raffinolactis, were positively correlated with steroid hormones and tryptophan metabolites, and their abundances declined obviously in the non-laying stage. Collectively, this study elaborates the holistic changes in serum biochemistry, gut metabolome and microbiome in geese at different reproductive stages. The dysregulation of amino acid and steroid hormone metabolism, combined with the loss of beneficial intestinal microbes, jointly induces the non-laying phenotype. This study provides new perspectives for understanding the gut–reproductive axis and supplies promising biomarkers to improve the laying performance of geese.